You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
the gene abundance of specified taxa can be extracted quickly and converted to MPSE. For example, the following codes will extract the gene abundance of Bifidobacterium, then re-calculate the total specified gene abundance according to the abundance of each contributed taxa, and generated a new MPSE object.
> mpse.ko2 %>% mp_extract_feature() %>% tidyr::unnest(contribute.taxa) %>% dplyr::filter(grepl('s__Bifidobact', contribute.taxa)) %>% dplyr::select(-contribute.taxa) %>% dplyr::group_by(OTU) %>% dplyr::summarize(dplyr::across(dplyr::everything(),sum)) %>% tibble::column_to_rownames(var='OTU') %>% MPSE() %>% dplyr::left_join(mpse.ko2 %>% mp_extract_sample())
# A MPSE-tibble (MPSE object) abstraction: 82,398 × 5
# OTU=886 | Samples=93 | Assays=Abundance | Taxonomy=NULL
OTU Sample Abundance geo_loc_name_country Group
<chr> <chr> <dbl> <chr> <chr>
1 K00001 SRR8849198 0 China PCOS
2 K00012 SRR8849198 8.03 China PCOS
3 K00013 SRR8849198 47.4 China PCOS
4 K00016 SRR8849198 51.8 China PCOS
5 K00031 SRR8849198 0 China PCOS
6 K00052 SRR8849198 40.5 China PCOS
7 K00053 SRR8849198 146. China PCOS
8 K00057 SRR8849198 0 China PCOS
9 K00058 SRR8849198 27.3 China PCOS
10 K00059 SRR8849198 5.59 China PCOS
# ℹ 82,388 more rows
# ℹ Use `print(n = ...)` to see more rows
The text was updated successfully, but these errors were encountered:
introduced
keep.contribute.abundance
argument inmp_import_humann_regroup()
6ccd981.The default
keep.contribute.abundance = FALSE
only the taxa information was kept.
keep.contribute.abundance=TRUE
the abundance of each contributed taxa in each sample will be kept, and they can be extract with
mp_extract_feature
.the gene abundance of specified taxa can be extracted quickly and converted to
MPSE
. For example, the following codes will extract the gene abundance of Bifidobacterium, then re-calculate the total specified gene abundance according to the abundance of each contributed taxa, and generated a newMPSE
object.The text was updated successfully, but these errors were encountered: